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Predicting ion channel conductance via dissipation-corrected targeted molecular dynamics and Langevin equation simulations

Authors
  • Jäger, Miriam
  • Koslowski, Thorsten
  • Wolf, Steffen
Type
Preprint
Publication Date
May 02, 2021
Submission Date
Apr 22, 2021
Source
DIALNET
License
Yellow
External links

Abstract

Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted MD in combination with LE simulations to potassium diffusion through the Gramicidin A channel as a test system. Performing a non-equilibrium principal component analysis on backbone dihedral angles, we find coupled protein-ion dynamics to occur during ion transfer. The dissipation-corrected free energy profiles correspond well to predictions from other biased simulation methods. Employing Langevin simulations taking into account an external electric field predicts macroscopic observables in the form of I-V characteristics, which exhibit good agreement with their experimental counterparts, but highlight the necessity to include polarization effects in ion diffusion simulations.

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